Re: [Rdkit-discuss] Cartridge upgrades

2017-12-08 Thread Tim Dudgeon 

Thanks Greg.
I hit some strange problems with similarity search not working after an 
upgrade (SSS seemed OK). I never really got to the bottom of this as I 
managed to solve it by deleting the RDKit artifacts from the database 
and dropping and reinstalling the cartridge and after that all works fine.



On 05/12/17 07:18, Greg Landrum wrote:


On Fri, Dec 1, 2017 at 7:24 PM, Tim Dudgeon > wrote:


If upgrading PostgreSQL to a new version of the RDKit cartridge is
any maintenance needed?

Either rebuild the indexes or regenerate the fingerprints and
rebuild the indexes?


It depend on the release. Usually you don't need to, but there are 
cases where it's required.

I normally try to capture this in the release notes.
For example, this was in the *important* section of the 2017.03.1 
release notes:


- The fix for bug #879 changes the definition of the layered
fingerprint.
  This means that all database columns using layered fingerprints
as well as
  all substructure search indices should be rebuilt.


Having said that, bug fixes that affect things like aromaticity 
perception could change some fingerprints and I don't always think to 
capture a specific note about changing fingerprints in these cases.


It's generally a good idea to go through the release notes before an 
upgrade in any case.


If the database isn't too big, regenerating fingerprints and indices 
isn't a terrible idea... just to be safe. :-)


-greg




--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Rajarshi Guha 
Thanks Greg.

Right now I have

rdkit 2017.09.2.0  py27h080088d_1rdkit

rdkit-postgresql  2016.03.3py27_1rdkit

But when I try to install the extension I get an error

chembl23=# create extension if not exists rdkit;

ERROR:  could not load library
"/home/rdkit/.conda/envs/ifx-rdkit-env/lib/postgresql/rdkit.so":
libAvalonLib.so.1: cannot open shared object file: No such file or directory

STATEMENT:  create extension if not exists rdkit;

ERROR:  could not load library
"/home/rdkit/.conda/envs/ifx-rdkit-env/lib/postgresql/rdkit.so":
libAvalonLib.so.1: cannot open shared object file: No such file or directory

Would this be related to the mismatch between the rdkit and rdkit-postgres
versions?

If so, what is the recommended way to get postgres to use the 2017 version
of rdkit?

On Fri, Dec 8, 2017 at 10:07 AM, Greg Landrum 
wrote:

> At some point, in the not too distant future (I hope), there will be an
> updated version of the cartridge.
>
> On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
> wrote:
>
>> Thanks Riccardo.
>>
>> While I can see Rdkit 2017.09.2.0 is available on conda (
>> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
>> at 2016.03.4
>>
>> Can I update the rdkit installation and use it to update the Postgres
>> extension? Or must I wait for a rdkit-postgres conda with the right version
>> of Rdkit?
>>
>> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
>> riccardo.viane...@gmail.com> wrote:
>>
>>> Hi Rajarshi,
>>>
>>> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha >> > wrote:
>>>
 Hi, I'm working on an application that is trying to do arbitrary
 substructure queries across ChEMBL 23. I pretty much followed the
 instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
 RAM.

>>>
>>> some 2016 releases were affected by a bug in the cartridge Makefile that
>>> disabled any compiler optimization. If possible, I would suggest trying a
>>> more recent version (>= 2016.09.1).
>>>
>>> Best,
>>> Riccardo
>>>
>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Greg Landrum 
At some point, in the not too distant future (I hope), there will be an
updated version of the cartridge.

On Fri, Dec 8, 2017 at 3:55 PM, Rajarshi Guha 
wrote:

> Thanks Riccardo.
>
> While I can see Rdkit 2017.09.2.0 is available on conda (
> https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
> at 2016.03.4
>
> Can I update the rdkit installation and use it to update the Postgres
> extension? Or must I wait for a rdkit-postgres conda with the right version
> of Rdkit?
>
> On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
> riccardo.viane...@gmail.com> wrote:
>
>> Hi Rajarshi,
>>
>> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
>> wrote:
>>
>>> Hi, I'm working on an application that is trying to do arbitrary
>>> substructure queries across ChEMBL 23. I pretty much followed the
>>> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
>>> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
>>> RAM.
>>>
>>
>> some 2016 releases were affected by a bug in the cartridge Makefile that
>> disabled any compiler optimization. If possible, I would suggest trying a
>> more recent version (>= 2016.09.1).
>>
>> Best,
>> Riccardo
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Postgres query performance

2017-12-08 Thread Rajarshi Guha 
Thanks Riccardo.

While I can see Rdkit 2017.09.2.0 is available on conda (
https://anaconda.org/search?q=rdkit), rdkit-postgres seems to be stuck
at 2016.03.4

Can I update the rdkit installation and use it to update the Postgres
extension? Or must I wait for a rdkit-postgres conda with the right version
of Rdkit?

On Thu, Nov 30, 2017 at 6:03 PM, Riccardo Vianello <
riccardo.viane...@gmail.com> wrote:

> Hi Rajarshi,
>
> On Thu, Nov 30, 2017 at 10:31 PM, Rajarshi Guha 
> wrote:
>
>> Hi, I'm working on an application that is trying to do arbitrary
>> substructure queries across ChEMBL 23. I pretty much followed the
>> instructions at http://www.rdkit.org/docs/Cartridge.html on a Postgres
>> 9.2 instance with RDKit 2016.03.1 all running on a Linux box with 88GB of
>> RAM.
>>
>
> some 2016 releases were affected by a bug in the cartridge Makefile that
> disabled any compiler optimization. If possible, I would suggest trying a
> more recent version (>= 2016.09.1).
>
> Best,
> Riccardo
>
>


-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss